Polishing

jlmaier12 · Dec 15, 2024 · 070e86c · 070e86c
1 parent 923916c
commit 070e86c
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Showing 7 changed files with 16 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,8 +30,10 @@ LazyData: false
 Imports: graphics, utils, stats, dplyr, ggplot2, patchwork, stringr, tidyr, roll
 RoxygenNote: 7.3.2
 biocViews: Coverage, Metagenomics, PatternLogic, Classification, Sequencing
+URL: https://github.com/jlmaier12/TrIdent 
 BugReports: https://github.com/jlmaier12/TrIdent/issues 
 Suggests: 
+    BiocStyle,
     knitr,
     rmarkdown,
     kableExtra,

diff --git a/R/patternMatcher.R b/R/patternMatcher.R
@@ -44,13 +44,13 @@ patternMatcher <-
             i <- contigNames[[p]]
             viralSubset <- VLPpileup[which(VLPpileup[, 1] == i), ]
             if (B == floor(length(contigNames) / 4)) {
-                message("A quarter of the way done with pattern matching")
+                message("A quarter of the way done with pattern-matching")
             }
             if (B == floor(length(contigNames) / 2)) {
-                message("Half of the way done with pattern matching")
+                message("Half of the way done with pattern-matching")
             }
             if (B == floor((length(contigNames) * 3) / 4)) {
-                message("Almost done with pattern matching!")
+                message("Almost done with pattern-matching!")
             }
             B <<- B + 1
             if (viralSubset[nrow(viralSubset), 3] < minContigLength) {

diff --git a/R/plotTrIdentResults.R b/R/plotTrIdentResults.R
@@ -104,8 +104,9 @@ plotTrIdentResults <- function(VLPpileup,
                 panel.background = element_blank(),
                 axis.line = element_line(colour = "black"),
                 text = element_text(size = 14),
-                axis.text = element_text(size = 10),
-                plot.subtitle = element_text(size = 11),
+                axis.text = element_text(size = 11),
+                plot.subtitle = element_text(size = 12),
+                plot.title = element_text(size = 14),
                 plot.margin = margin(
                     t = 0,
                     r = 6,
@@ -131,7 +132,7 @@ plotTrIdentResults <- function(VLPpileup,
                 panel.background = element_blank(),
                 axis.line = element_line(colour = "black"),
                 text = element_text(size = 14),
-                axis.text = element_text(size = 10),
+                axis.text = element_text(size = 11),
                 plot.margin = margin(
                     t = 0,
                     r = 6,

diff --git a/R/resultsHisto.R b/R/resultsHisto.R
@@ -59,9 +59,9 @@ resultsHisto <- function(summaryList, suggFiltThresh) {
                 plot.title = element_text(size = 16),
                 axis.text = element_text(size = 12),
                 axis.title = element_text(size = 12),
-                plot.caption = element_text(size = 11),
+                plot.caption = element_text(size = 12),
                 legend.title = element_text(size = 12),
-                legend.text = element_text(size = 11)
+                legend.text = element_text(size = 12)
             )
     } else {
         plot <- ggplot(data = cleanSummaryTable) +

diff --git a/R/specTransductionPlot.R b/R/specTransductionPlot.R
@@ -82,11 +82,11 @@ specTransductionPlot <-
                 theme(
                     panel.grid.major = element_blank(),
                     panel.grid.minor = element_blank(),
-                    plot.subtitle = element_text(size = 11),
+                    plot.subtitle = element_text(size = 12),
                     panel.background = element_blank(),
                     axis.line = element_line(colour = "black"),
                     text = element_text(size = 15),
-                    plot.title = element_text(size = 12)
+                    plot.title = element_text(size = 14)
                 ) +
                 labs(
                     title = paste(

diff --git a/man/TrIdent-package.Rd b/man/TrIdent-package.Rd
diff --git a/vignettes/TrIdent-vignette.Rmd b/vignettes/TrIdent-vignette.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "TrIdent"
-author: "Jessie Maier & Jorden Rabasco"
+author: "Jessie Maier, Jorden Rabasco"
 output:
   BiocStyle::html_document:
     toc: true
@@ -17,9 +17,7 @@ vignette: >
 
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
-    fig.width = 9,
-    fig.asp = 0.8,
-    out.width = "85%",
+    out.width = "90%",
     collapse = TRUE,
     comment = "##"
 )